All cells after denoising

Major cell types

Only major cell types

## [1] "Endothelial" "Epithelial"  "Immune"      "Mesenchymal"

Major cell types and immune subtypes and T cells as a group

## [1] "Endothelial"  "Epithelial"   "Mesenchymal"  "Myeloid"      "NK_cells"    
## [6] "Other_immune" "T_cells"

Subtypes

All subtypes

##  [1] "Endothelial"   "Epithelial_1"  "Epithelial_10" "Epithelial_2" 
##  [5] "Epithelial_3"  "Epithelial_4"  "Epithelial_5"  "Epithelial_6" 
##  [9] "Epithelial_7"  "Epithelial_8"  "Epithelial_9"  "Mesenchymal"  
## [13] "Myeloid"       "NK_cells"      "Other_immune"  "T_cells"      
## [17] "Tc_cells"      "Th_cells"

Subtypes (T cells as one group)

##  [1] "Endothelial"   "Epithelial_1"  "Epithelial_10" "Epithelial_2" 
##  [5] "Epithelial_3"  "Epithelial_4"  "Epithelial_5"  "Epithelial_6" 
##  [9] "Epithelial_7"  "Epithelial_8"  "Epithelial_9"  "Mesenchymal"  
## [13] "Myeloid"       "NK_cells"      "Other_immune"  "T_cells"

Only Immune

All subtypes

## [1] "Myeloid"      "NK_cells"     "Other_immune" "T_cells"      "Tc_cells"    
## [6] "Th_cells"

Subtypes (T cells as one group)

## [1] "Myeloid"      "NK_cells"     "Other_immune" "T_cells"

Only Epithelial

All Epithelial subtypes

##  [1] "Epithelial_1"  "Epithelial_10" "Epithelial_2"  "Epithelial_3" 
##  [5] "Epithelial_4"  "Epithelial_5"  "Epithelial_6"  "Epithelial_7" 
##  [9] "Epithelial_8"  "Epithelial_9"

Stromal cells only

All subtypes

## [1] "Endothelial"  "Mesenchymal"  "Myeloid"      "NK_cells"     "Other_immune"
## [6] "T_cells"      "Tc_cells"     "Th_cells"

Subtypes (T cells as one group)

## [1] "Endothelial"  "Mesenchymal"  "Myeloid"      "NK_cells"     "Other_immune"
## [6] "T_cells"

Exploring Rh negative only

Major cell types

Only major cell types

## [1] "Endothelial" "Epithelial"  "Immune"      "Mesenchymal"

Major cell types and immune subtypes and T cells as a group

## [1] "Endothelial"  "Epithelial"   "Mesenchymal"  "Myeloid"      "NK_cells"    
## [6] "Other_immune" "T_cells"

Subtypes

All subtypes

##  [1] "Endothelial"   "Epithelial_1"  "Epithelial_10" "Epithelial_2" 
##  [5] "Epithelial_3"  "Epithelial_4"  "Epithelial_5"  "Epithelial_6" 
##  [9] "Epithelial_7"  "Epithelial_8"  "Epithelial_9"  "Mesenchymal"  
## [13] "Myeloid"       "NK_cells"      "Other_immune"  "T_cells"      
## [17] "Tc_cells"      "Th_cells"

Subtypes (T cells as one group)

##  [1] "Endothelial"   "Epithelial_1"  "Epithelial_10" "Epithelial_2" 
##  [5] "Epithelial_3"  "Epithelial_4"  "Epithelial_5"  "Epithelial_6" 
##  [9] "Epithelial_7"  "Epithelial_8"  "Epithelial_9"  "Mesenchymal"  
## [13] "Myeloid"       "NK_cells"      "Other_immune"  "T_cells"

Only Immune

All subtypes

## [1] "Myeloid"      "NK_cells"     "Other_immune" "T_cells"      "Tc_cells"    
## [6] "Th_cells"

Subtypes (T cells as one group)

## [1] "Myeloid"      "NK_cells"     "Other_immune" "T_cells"

Only Epithelial

All Epithelial subtypes

##  [1] "Epithelial_1"  "Epithelial_10" "Epithelial_2"  "Epithelial_3" 
##  [5] "Epithelial_4"  "Epithelial_5"  "Epithelial_6"  "Epithelial_7" 
##  [9] "Epithelial_8"  "Epithelial_9"

Stromal cells only

All subtypes

## [1] "Endothelial"  "Mesenchymal"  "Myeloid"      "NK_cells"     "Other_immune"
## [6] "T_cells"      "Tc_cells"     "Th_cells"

Subtypes (T cells as one group)

## [1] "Endothelial"  "Mesenchymal"  "Myeloid"      "NK_cells"     "Other_immune"
## [6] "T_cells"

Exploring Rh positive only

Major cell types

Only major cell types

## [1] "Endothelial" "Epithelial"  "Immune"      "Mesenchymal"

Major cell types and immune subtypes and T cells as a group

## [1] "Endothelial"  "Epithelial"   "Mesenchymal"  "Myeloid"      "NK_cells"    
## [6] "Other_immune" "T_cells"

Subtypes

All subtypes

##  [1] "Endothelial"   "Epithelial_1"  "Epithelial_10" "Epithelial_2" 
##  [5] "Epithelial_3"  "Epithelial_4"  "Epithelial_5"  "Epithelial_6" 
##  [9] "Epithelial_7"  "Epithelial_8"  "Epithelial_9"  "Mesenchymal"  
## [13] "Myeloid"       "NK_cells"      "Other_immune"  "T_cells"      
## [17] "Tc_cells"      "Th_cells"

Subtypes (T cells as one group)

##  [1] "Endothelial"   "Epithelial_1"  "Epithelial_10" "Epithelial_2" 
##  [5] "Epithelial_3"  "Epithelial_4"  "Epithelial_5"  "Epithelial_6" 
##  [9] "Epithelial_7"  "Epithelial_8"  "Epithelial_9"  "Mesenchymal"  
## [13] "Myeloid"       "NK_cells"      "Other_immune"  "T_cells"

Only Immune

All subtypes

## [1] "Myeloid"      "NK_cells"     "Other_immune" "T_cells"      "Tc_cells"    
## [6] "Th_cells"

Subtypes (T cells as one group)

## [1] "Myeloid"      "NK_cells"     "Other_immune" "T_cells"

Only Epithelial

All Epithelial subtypes

##  [1] "Epithelial_1"  "Epithelial_10" "Epithelial_2"  "Epithelial_3" 
##  [5] "Epithelial_4"  "Epithelial_5"  "Epithelial_6"  "Epithelial_7" 
##  [9] "Epithelial_8"  "Epithelial_9"

Stromal cells only

All subtypes

## [1] "Endothelial"  "Mesenchymal"  "Myeloid"      "NK_cells"     "Other_immune"
## [6] "T_cells"      "Tc_cells"     "Th_cells"

Subtypes (T cells as one group)

## [1] "Endothelial"  "Mesenchymal"  "Myeloid"      "NK_cells"     "Other_immune"
## [6] "T_cells"

Cell types afected by removal of Rh+

## Total number of cells:  1721027
## Rh Negative number of cells:  111593
## Rh Positive number of cells:  1609434
## % of cells presumably lost in previous analysis:  93.51591 %

Total cell types percentages:

## 
## Endothelial  Epithelial      Immune Mesenchymal 
##    1.710607   47.305068   29.614004   21.370321
## 
##   Endothelial  Epithelial_1 Epithelial_10  Epithelial_2  Epithelial_3 
##      1.710607      9.235706      2.483750      2.696878      6.562709 
##  Epithelial_4  Epithelial_5  Epithelial_6  Epithelial_7  Epithelial_8 
##      1.325023      6.058185      7.575302      4.071058      6.303271 
##  Epithelial_9   Mesenchymal       Myeloid      NK_cells  Other_immune 
##      0.993186     21.370321      4.414399      1.943258     14.041209 
##       T_cells      Tc_cells      Th_cells 
##      6.705241      1.100971      1.408926
## 
##   Endothelial  Epithelial_1 Epithelial_10  Epithelial_2  Epithelial_3 
##      1.710607      9.235706      2.483750      2.696878      6.562709 
##  Epithelial_4  Epithelial_5  Epithelial_6  Epithelial_7  Epithelial_8 
##      1.325023      6.058185      7.575302      4.071058      6.303271 
##  Epithelial_9   Mesenchymal       Myeloid      NK_cells  Other_immune 
##      0.993186     21.370321      4.414399      1.943258     14.041209 
##       T_cells 
##      9.215137
## 
##  Endothelial   Epithelial  Mesenchymal      Myeloid     NK_cells Other_immune 
##     1.710607    47.305068    21.370321     4.414399     1.943258    14.041209 
##      T_cells 
##     9.215137

Rh negative cell types percentages:

## 
## Endothelial  Epithelial      Immune Mesenchymal 
##    1.536835   24.675383   48.145493   25.642289
## 
##   Endothelial  Epithelial_1 Epithelial_10  Epithelial_2  Epithelial_3 
##     1.5368347     0.3450037     0.6891113     0.8898408     1.8881113 
##  Epithelial_4  Epithelial_5  Epithelial_6  Epithelial_7  Epithelial_8 
##     0.7491509     3.4132965     0.1155986     5.1983547     3.5073885 
##  Epithelial_9   Mesenchymal       Myeloid      NK_cells  Other_immune 
##     7.8795265    25.6422894    13.2526234     1.6846935     5.9708046 
##       T_cells      Tc_cells      Th_cells 
##     3.2591650    10.9057020    13.0725045
## 
##   Endothelial  Epithelial_1 Epithelial_10  Epithelial_2  Epithelial_3 
##     1.5368347     0.3450037     0.6891113     0.8898408     1.8881113 
##  Epithelial_4  Epithelial_5  Epithelial_6  Epithelial_7  Epithelial_8 
##     0.7491509     3.4132965     0.1155986     5.1983547     3.5073885 
##  Epithelial_9   Mesenchymal       Myeloid      NK_cells  Other_immune 
##     7.8795265    25.6422894    13.2526234     1.6846935     5.9708046 
##       T_cells 
##    27.2373715
## 
##  Endothelial   Epithelial  Mesenchymal      Myeloid     NK_cells Other_immune 
##     1.536835    24.675383    25.642289    13.252623     1.684693     5.970805 
##      T_cells 
##    27.237372

Rh positive cell types percentages:

## 
## Endothelial  Epithelial      Immune Mesenchymal 
##    1.722655   48.874138   28.329090   21.074117
## 
##   Endothelial  Epithelial_1 Epithelial_10  Epithelial_2  Epithelial_3 
##     1.7226553     9.8521592     2.6081840     2.8221723     6.8868310 
##  Epithelial_4  Epithelial_5  Epithelial_6  Epithelial_7  Epithelial_8 
##     1.3649519     6.2415731     8.0925344     3.9928944     6.4971288 
##  Epithelial_9   Mesenchymal       Myeloid      NK_cells  Other_immune 
##     0.5157092    21.0741167     3.8015849     1.9611864    14.6007851 
##       T_cells      Tc_cells      Th_cells 
##     6.9441804     0.4211418     0.6002110
## 
##   Endothelial  Epithelial_1 Epithelial_10  Epithelial_2  Epithelial_3 
##     1.7226553     9.8521592     2.6081840     2.8221723     6.8868310 
##  Epithelial_4  Epithelial_5  Epithelial_6  Epithelial_7  Epithelial_8 
##     1.3649519     6.2415731     8.0925344     3.9928944     6.4971288 
##  Epithelial_9   Mesenchymal       Myeloid      NK_cells  Other_immune 
##     0.5157092    21.0741167     3.8015849     1.9611864    14.6007851 
##       T_cells 
##     7.9655332
## 
##  Endothelial   Epithelial  Mesenchymal      Myeloid     NK_cells Other_immune 
##     1.722655    48.874138    21.074117     3.801585     1.961186    14.600785 
##      T_cells 
##     7.965533

Heatmaps

All cells

Rh negative

Rh positive

Other Comparisons

## 
## Attaching package: 'dplyr'
## The following objects are masked from 'package:stats':
## 
##     filter, lag
## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union
## Using pt_ID, CANARY, CD90, cell_type, subtype, subtype2, subtype3 as id variables

## Using pt_ID, CANARY, CD90, cell_type, subtype, subtype2, subtype3 as id variables

## Using pt_ID, CANARY, CD90, cell_type, subtype, subtype2, subtype3 as id variables

## Using pt_ID, CANARY, CD90, cell_type, subtype, subtype2, subtype3 as id variables

## Using pt_ID, CANARY, CD90, cell_type, subtype, subtype2, subtype3 as id variables

## Using pt_ID, CANARY, CD90, cell_type, subtype, subtype2, subtype3 as id variables

## Using pt_ID, CANARY, CD90, cell_type, subtype, subtype2, subtype3 as id variables

## Using pt_ID, CANARY, CD90, cell_type, subtype, subtype2, subtype3 as id variables

## Using pt_ID, CANARY, CD90, cell_type, subtype, subtype2, subtype3 as id variables